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vcf

Overview

Field Value
Format key vcf
Spec file formats/vcf.json
Cite name GWAS-VCF
Version 20220923
Source https://github.com/MRCIEU/gwas-vcf-specification/tree/1.0.0
GitHub https://github.com/MRCIEU/gwas-vcf-specification
Citation Lyon, M.S., Andrews, S.J., Elsworth, B. et al. The variant call format provides efficient and robust storage of GWAS summary statistics. Genome Biol 22, 32 (2021). https://doi.org/10.1186/s13059-020-02248-0
## Column mapping
Raw header Canonical Canonical (secondary)
#CHROM CHR —
AF EAF —
ALT EA —
ES BETA —
EZ Z —
ID SNPID rsID
LP MLOG10P —
POS POS —
REF NEA —
SE SE —
SI INFO —
SS N —
## Fixed columns

Required columns: #CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT FORMAT fields (VCF): ID, SS, ES, SE, LP, SI, EZ

Fixed header block ``` ##fileformat=VCFv4.2 ##FILTER= ##INFO= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##META= ##META= ##META= ##META= ##META= ##META= ##META= ##META= ```
GRCh37 contig headers ``` ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ```
GRCh38 contig headers ``` ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ```

Coverage

9/9 tier groups satisfied.

Tier Status Matched Missing
Variant ID yes SNPID, rsID —
Genomic location yes CHR, POS —
Effect / other allele yes EA, NEA —
Effect size yes BETA, Z OR, HR
Uncertainty yes SE —
P-value yes MLOG10P P
Sample size yes N N_CASE
Allele frequency yes EAF MAF, NEAF
Imputation / QC yes INFO —
## See also